Hi Jason,I want to protonate the N3 of the base of the nucleic CYT 62. After i loadoff the all_pronate_nucleic10.lib, but i can not save the parameter force field use the saveamberparm. the error is : For atom: R<CP 62>. A <C6 14> could not find type; C1
For atom: R<CP 62>. A <C5 16> could not find type; C1
Parameter file was not saved.
when i use the loadAmberParams frcmod.protonated_nucleic, the error is same.
thank you!
At 2014-05-28 09:00:20, "王珍" <wangzhenzk.126.com> wrote:
>
>
>Hi Jason,
>Thank you for your help. I solved the problem based on your suggestion. thank you!
>
>
>
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>
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>At 2014-05-27 06:20:14, "Jason Swails" <jason.swails.gmail.com> wrote:
>>On Tue, May 27, 2014 at 3:08 AM, 王珍 <wangzhenzk.126.com> wrote:
>>
>>> Hi Sir,
>>>
>>> Recently I use the Ambertools12 to protonate the N3 of the base Cytosine62
>>> of the nucleic, I find the model of pdb at the
>>> AmberTools12/amber12/dat/leap/prep/protonated_nucleic/RC+.pdb. but I do not
>>> realize how can I call the model to add the hydrogen according the RC+.pdb.
>>>
>>> I will deeply appreciate if you would like to tell me the solution.
>>>
>>
>>The protonated nucleic acids can be loaded into your leap session using
>>the command "loadOFF all_prot_nucleic10.lib". At that point, if you rename
>>the C 62 residue "CP" in your nucleic acid PDB file, leap will add
>>hydrogens according to the protonated Cytosine template.
>>
>>HTH,
>>Jason
>>
>>--
>>Jason M. Swails
>>BioMaPS,
>>Rutgers University
>>Postdoctoral Researcher
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Received on Wed May 28 2014 - 08:00:03 PDT
